Helitron_like_N - PFAM28P - GREMLIN Contacts

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Helitron_like_N - Helitron helicase-like domain at N-terminus

PFAM:	PF14214	Sequences: YYAYRLQGRFAEDPTFLLLAGRLFQQYIVDAYARIESNRLNYIRKNQKKLRAELYTGEELQDALENGDTDGASLLGKRVILPSSFTGSPRYMKQLYQDAMAIVRHFGKPDLFITFTCNPKWPEITRLLELPGNQTAADRPDIVARVFHLKLKALLKDLLKKGIFGKVVAYVYRIEFQKRGLPHAHILL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (182)
Sequences:	3051 (2404)
Seq/√Len:	178.2
META:	0.656

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
148_H	152_K	5.066	1.00
151_L	184_A	4.518	1.00
115_F	154_L	4.275	1.00
147_F	174_I	3.466	1.00
46_N	49_K	3.324	1.00
122_P	126_R	3.173	1.00
91_Y	95_L	2.736	1.00
120_K	125_T	2.644	1.00
106_F	169_A	2.621	1.00
156_K	160_K	2.380	1.00
172_Y	184_A	2.370	1.00
153_A	157_D	2.348	1.00
130_L	134_Q	2.299	1.00
176_F	182_P	2.212	1.00
159_L	167_V	2.176	1.00
41_N	45_K	2.157	1.00
86_T	91_Y	2.076	1.00
85_F	88_S	2.040	1.00
155_L	186_I	2.008	1.00
136_A	143_V	1.966	1.00
127_L	142_I	1.965	1.00
111_L	164_F	1.841	1.00
52_A	55_Y	1.813	1.00
18_L	24_F	1.702	1.00
96_Y	100_M	1.698	1.00
41_N	44_R	1.677	1.00
103_V	109_P	1.644	1.00
121_W	150_K	1.623	1.00
93_K	97_Q	1.614	1.00
156_K	161_K	1.601	1.00
32_Y	36_E	1.550	1.00
24_F	28_I	1.538	1.00
35_I	39_R	1.522	1.00
158_L	188_L	1.519	1.00
6_L	28_I	1.506	1.00
162_G	166_K	1.506	1.00
95_L	98_D	1.500	1.00
119_P	181_L	1.493	1.00
117_C	121_W	1.479	1.00
151_L	186_I	1.474	1.00
57_G	62_D	1.473	1.00
47_Q	50_L	1.472	1.00
92_M	173_R	1.439	1.00
159_L	162_G	1.424	1.00
174_I	184_A	1.419	1.00
51_R	54_L	1.391	1.00
117_C	124_I	1.331	1.00
109_P	187_L	1.329	1.00
36_E	85_F	1.321	1.00
31_A	34_R	1.314	1.00
83_S	94_Q	1.310	1.00
33_A	37_S	1.303	1.00
99_A	171_V	1.292	1.00
174_I	182_P	1.273	1.00
102_I	169_A	1.265	1.00
149_L	153_A	1.255	1.00
118_N	121_W	1.255	1.00
27_Y	31_A	1.238	1.00
103_V	108_K	1.230	1.00
155_L	159_L	1.220	1.00
54_L	57_G	1.211	1.00
43_I	82_P	1.204	1.00
113_I	188_L	1.192	1.00
147_F	182_P	1.185	1.00
50_L	55_Y	1.185	1.00
91_Y	173_R	1.184	1.00
177_Q	182_P	1.171	1.00
4_Y	7_Q	1.164	1.00
37_S	88_S	1.145	1.00
42_Y	49_K	1.144	1.00
22_R	26_Q	1.142	1.00
113_I	186_I	1.140	1.00
63_A	67_G	1.130	1.00
167_V	170_Y	1.124	1.00
139_R	142_I	1.115	1.00
42_Y	46_N	1.114	1.00
68_D	71_G	1.107	1.00
10_F	13_D	1.102	1.00
176_F	180_G	1.082	1.00
115_F	151_L	1.082	1.00
123_E	150_K	1.081	1.00
134_Q	138_D	1.080	1.00
47_Q	51_R	1.077	1.00
22_R	25_Q	1.069	1.00
125_T	136_A	1.067	1.00
151_L	172_Y	1.066	1.00
26_Q	29_V	1.063	1.00
28_I	31_A	1.057	1.00
159_L	170_Y	1.056	1.00
131_P	134_Q	1.037	1.00
102_I	106_F	1.032	0.99
154_L	159_L	1.026	0.99
12_E	138_D	1.023	0.99
38_N	45_K	0.999	0.99
57_G	61_Q	0.991	0.99
43_I	46_N	0.983	0.99
155_L	172_Y	0.983	0.99
29_V	33_A	0.960	0.99
44_R	47_Q	0.956	0.99
56_T	63_A	0.954	0.99
128_L	142_I	0.953	0.99
8_G	11_A	0.953	0.99
36_E	39_R	0.952	0.99
153_A	156_K	0.951	0.99
67_G	73_S	0.949	0.99
157_D	161_K	0.946	0.99
178_K	181_L	0.945	0.99
94_Q	98_D	0.929	0.99
32_Y	35_I	0.915	0.99
80_I	83_S	0.913	0.99
56_T	60_L	0.913	0.99
142_I	150_K	0.907	0.99
158_L	164_F	0.901	0.99
153_A	161_K	0.896	0.99
81_L	90_R	0.888	0.98
95_L	102_I	0.886	0.98
12_E	15_T	0.882	0.98
13_D	19_L	0.882	0.98
98_D	171_V	0.874	0.98
38_N	42_Y	0.873	0.98
148_H	151_L	0.871	0.98
36_E	40_L	0.865	0.98
177_Q	181_L	0.864	0.98
20_A	25_Q	0.863	0.98
129_E	135_T	0.850	0.98
38_N	41_N	0.847	0.98
35_I	42_Y	0.846	0.98
95_L	99_A	0.830	0.98
42_Y	50_L	0.828	0.98
101_A	104_R	0.822	0.97
165_G	169_A	0.821	0.97
39_R	43_I	0.810	0.97
5_R	27_Y	0.809	0.97
17_L	24_F	0.803	0.97
134_Q	139_R	0.801	0.97
37_S	43_I	0.797	0.97
26_Q	36_E	0.795	0.97
62_D	66_N	0.795	0.97
60_L	97_Q	0.793	0.97
8_G	130_L	0.791	0.97
61_Q	65_E	0.790	0.97
5_R	12_E	0.785	0.97
43_I	50_L	0.769	0.96
3_A	19_L	0.766	0.96
53_E	57_G	0.766	0.96
40_L	43_I	0.762	0.96
11_A	139_R	0.753	0.96
128_L	134_Q	0.751	0.96
82_P	90_R	0.745	0.96
20_A	24_F	0.736	0.95
68_D	72_A	0.736	0.95
14_P	18_L	0.733	0.95
147_F	151_L	0.727	0.95
117_C	143_V	0.722	0.95
26_Q	30_D	0.718	0.95
161_K	164_F	0.715	0.94
15_T	19_L	0.712	0.94
4_Y	8_G	0.712	0.94
42_Y	45_K	0.707	0.94
141_D	145_R	0.701	0.94
98_D	118_N	0.697	0.94
144_A	149_L	0.693	0.93
116_T	177_Q	0.691	0.93
46_N	50_L	0.689	0.93
45_K	49_K	0.686	0.93
37_S	41_N	0.685	0.93
3_A	6_L	0.677	0.93
18_L	136_A	0.670	0.92
88_S	186_I	0.668	0.92
154_L	158_L	0.668	0.92
67_G	72_A	0.663	0.92
17_L	25_Q	0.661	0.92
130_L	135_T	0.656	0.91
71_G	75_L	0.654	0.91
62_D	65_E	0.651	0.91
37_S	40_L	0.648	0.91
36_E	42_Y	0.647	0.91
74_L	78_R	0.637	0.90
48_K	52_A	0.636	0.90
6_L	18_L	0.636	0.90
111_L	171_V	0.634	0.90
145_R	149_L	0.634	0.90
149_L	152_K	0.629	0.90
173_R	181_L	0.627	0.90
56_T	62_D	0.625	0.89
119_P	177_Q	0.625	0.89
175_E	183_H	0.622	0.89
18_L	25_Q	0.621	0.89
6_L	10_F	0.620	0.89
53_E	56_T	0.617	0.89
48_K	73_S	0.614	0.89
162_G	167_V	0.611	0.88
74_L	107_G	0.608	0.88
92_M	95_L	0.607	0.88
51_R	55_Y	0.604	0.88
63_A	66_N	0.602	0.88
34_R	38_N	0.602	0.88
28_I	32_Y	0.601	0.87
46_N	55_Y	0.601	0.87
157_D	163_I	0.595	0.87
132_G	135_T	0.588	0.86
80_I	90_R	0.588	0.86
34_R	40_L	0.587	0.86
23_L	116_T	0.586	0.86
57_G	63_A	0.586	0.86
87_G	92_M	0.580	0.86
7_Q	10_F	0.573	0.85
95_L	137_A	0.573	0.85
5_R	8_G	0.571	0.85
102_I	140_P	0.570	0.85
7_Q	18_L	0.569	0.84
3_A	7_Q	0.569	0.84
60_L	106_F	0.567	0.84
39_R	42_Y	0.565	0.84
50_L	53_E	0.565	0.84
150_K	173_R	0.565	0.84
67_G	70_D	0.564	0.84
34_R	37_S	0.561	0.84
12_E	17_L	0.560	0.84
33_A	36_E	0.560	0.84
115_F	184_A	0.559	0.83
10_F	18_L	0.558	0.83
167_V	188_L	0.558	0.83
56_T	64_L	0.558	0.83
76_G	118_N	0.557	0.83
102_I	171_V	0.555	0.83
96_Y	157_D	0.555	0.83
106_F	168_V	0.554	0.83
137_A	151_L	0.551	0.83
8_G	13_D	0.550	0.82
37_S	44_R	0.549	0.82
175_E	185_H	0.549	0.82
31_A	38_N	0.548	0.82
128_L	131_P	0.548	0.82
27_Y	34_R	0.546	0.82
83_S	89_P	0.544	0.82
109_P	113_I	0.543	0.82
124_I	146_V	0.540	0.81
8_G	12_E	0.539	0.81
31_A	35_I	0.539	0.81
144_A	176_F	0.538	0.81
56_T	66_N	0.538	0.81
76_G	113_I	0.537	0.81
103_V	187_L	0.536	0.81
45_K	66_N	0.536	0.81
87_G	180_G	0.536	0.81
33_A	155_L	0.535	0.81
13_D	29_V	0.530	0.80
35_I	40_L	0.529	0.80
138_D	142_I	0.527	0.80
21_G	25_Q	0.527	0.80
22_R	27_Y	0.525	0.79
19_L	22_R	0.524	0.79
117_C	173_R	0.522	0.79
117_C	181_L	0.522	0.79
76_G	112_F	0.522	0.79
183_H	187_L	0.521	0.79
65_E	74_L	0.520	0.79
66_N	72_A	0.519	0.79
97_Q	104_R	0.519	0.79
21_G	24_F	0.519	0.79
13_D	17_L	0.519	0.79
158_L	167_V	0.519	0.79
109_P	117_C	0.516	0.78
8_G	28_I	0.513	0.78
104_R	112_F	0.505	0.77
23_L	26_Q	0.504	0.77
10_F	28_I	0.503	0.77
26_Q	34_R	0.501	0.76
165_G	178_K	0.501	0.76
74_L	135_T	0.500	0.76
87_G	124_I	0.500	0.76
5_R	17_L	0.500	0.76

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1l2mA	1	0.3138	23.3	0.934	Contact Map
2hwtA	1	0.2394	9.8	0.944	Contact Map
2hw0A	1	0.2872	7.1	0.948	Contact Map
1m55A	1	0.4681	4.5	0.952	Contact Map
3bxwB	2	0.2819	3.3	0.955	Contact Map
1ny71	4	0.3351	3.1	0.956	Contact Map
1h1jS	1	0.234	2.6	0.958	Contact Map
3mwmA	2	0.4149	2.5	0.958	Contact Map
4pp4A	1	0.6383	2.4	0.958	Contact Map
2fe3A	2	0.4894	2.4	0.959	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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